Sequence Read Archive

Stores raw sequence data from next-generation sequencing (NGS) technologies. SRA is a database which works as a core infrastructure for sharing of pre-publication sequence data, with the aim to make sequence data available to the research community to enhance reproducibility and allow for new discoveries by comparing data sets. The database also stores alignment information in the form of read placements on a reference sequence.

SRA citations

[…] e species that have (T. chinensis) or potentially have (M. californicus and Desmodus rotundus) three or more CHIAs in their genomes (tables S1 and S3). These libraries have been deposited into NCBI’s Sequence Read Archive, so we queried them via NCBI’s BLAST interface. We BLASTed (megablast) all five of the assembled T. chinensis CHIA paralogs against a pancreas library (). M. californicus and D. […]

[…] for mouse liver using Bowtie2, and filtered according to alignment scores using SAMtools. SRA files were converted to FASTQ format using the command fastq-dump in the SRA Toolkit (https://github.com/ncbi/sra-tools) before the alignment. Peaks were called using MACS2 without the --broad option and filtered with the criterion that the enrichment Q-value is smaller than 10−5. H3K4me3 peaks bound by […]

call_split

Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

[…] The 16S rRNA gene sequencing data were previously published (). Raw sequences were deposited in the NCBI Sequence Read Archive under project accession number PRJNA284355, and processed data files are available in the work of Burns et al. (). Briefly, total DNA was extracted from approximately 100 mg of t […]

library_books

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes

Genetic diversity and virulence profiles of Listeria monocytogenes recovered from bulk tank milk, milk filters, and milking equipment from dairies in the USA (2002 to 2014)

[…] nomes were sequenced by using 250-bp paired-end libraries, with a MiSeq reagent kit (v2), on a MiSeq system (Illumina), per the manufacturer's instructions. Raw sequencing reads were deposited in the NCBI SRA database under BioProject PRJNA215355 (Listeria monocytogenes database, US Food and Drug Administration GenomeTrakr Project) (). Sequencing contaminants were trimmed and removed using Trimmom […]

[…] The data analysis process of this research is summarized in Fig. . First, to identify circRNA, transcriptome sequencing data sets were obtained from the NCBI Sequence Read Archive (SRA). The back-spliced junction sites in each RNA-seq sample were identified using a circRNA discovery pipeline adapting the scripts provided on circBase [, ], which was referre […]

Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research
Organization of Information and Systems, Yata, Mishima, Japan; National Center for Biotechnology
Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

SRA funding source(s)

Supported by the DNA Data Bank of Japan, Ministry of Education, Culture, Sports, Science and Technology of Japan, the European Molecular Biology Laboratory, the European Commission and the Wellcome Trust, the National Library of Medicine, and Intramural Research Program of the NIH.

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